Skip to main content

Table 2 tSMS sequencing of ancient DNA extracts from sample TP (13,389 ± 52BP)

From: Improving the performance of true single molecule sequencing for ancient DNA

Sample Platform # Conditions #Seqs nucDNA bp mtDNA bp %Endo.
TP1 110 V 1 80°C, Phosphatase 1,980,210 85,738 2,885,229 53 1,845 4.33%
  110 V 1 80°C 234,094 28,797 998,007 8 255 12.30%
  110 V 1 95°C 228,871 12,573 438,111 5 162 5.50%
TP1RE 110 V 1 80°C, Phosphatase 1,607,848 161,284 5,597,277 99 3,378 10.04%
  550 V 8 80°C, Phosphatase 16,290,720 1,480,012 46,444,135 935 29,637 9.09%
  110 V 1 80°C 214,070 48,304 1,718,507 29 991 22.58%
  110 V 1 95°C 356,586 51,052 1,798,348 31 1,169 14.33%
TP2 110 V 1 80°C, Phosphatase 2,088,705 177,944 6,147,860 50 1,713 8.52%
  110 V 1 80°C 216,159 53,463 1,879,011 16 560 24.74%
  110 V 1 95°C 354,155 62,259 2,170,975 15 516 17.58%
TP2RE 110 V 1 80°C, Phosphatase 233,613 32,045 1,094,783 10 318 13.72%
  110 V 1 80°C 213,958 59,530 2,072,120 26 928 27.84%
  110 V 1 95°C 247,784 55,848 1,939,018 22 781 22.55%
  1. Sample TP was extracted in duplicate, and identical volumes of the extracts were tSMS sequenced on Helicos 110 FOV channels following different template preparation procedures as described in the methods section. The total number of sequences (#Seqs) as well as the number of hits mapping the horse reference nuclear (nucDNA) and mitochondrial (mtDNA) genome with mapping qualities higher than 25 but with no hit on the human reference genomes hg19 and rCRS are reported. The total sequence length covered by these reads is indicated in bp. The fraction of endogenous reads is estimated by summing the number of reads identified in nucDNA and mtDNA and dividing by the total number of reads generated per channel.